Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A1 F2 I198 R1 96 36.2 2313912 84.6% 1957569 85.2

Breseq alignment

N/A

GATK/CNVnator alignment

BRESEQ :: bam2aln output
CGCCAGAGAAATACTCCGCGCGGCGTGGGTAGTTAAATGACAGCGTTGCCAGCGCATCGAGGATGCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTTCAACGCCGATAATCCCGACGATAATTTCCGGCGGTACTCCATACACCTGCCACGCGCGATTCAACGCATCTTCATACTGATTCCAGA  >  NZ_CP009273/2818353‑2818538
                                                                                                  |                                                                                       
CGCCAGAGAAATACTCCGCGCGGCGTGGGTAGTTAAATGACAGCGTTGCCAGCGCATCGAGGATGCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTCC                                                                                        >  SRR3722077.918880/1‑100 (MQ=60)
  CCAGAGAAATACTCCGCGCGGCGTGGGTAGTTAAATGACAGCGTTGCCAGCGCATCGAGGATGCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTCCAA                                                                                      >  SRR3722077.512360/1‑100 (MQ=60)
                     GGCGTGGGTAGTTAAATGACAGCGTTGCCAGCGCATCGAGGATGCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTTCAACGCCGATAATCCCGACGAT                                                                   >  SRR3722077.450331/1‑100 (MQ=60)
                              AGTTAAATGACAGCGTTGCCAGCGCATCGAGGATGCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTCCAACGCCGATAATCCCGACGATAATTTCCGG                                                          >  SRR3722077.1024878/1‑100 (MQ=60)
                               GTTAAATGACAGCGTTGCCAGCGCATCGAGGATGCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTCCAACGCCGATAATCCCGACGATAATTTCCGGC                                                         >  SRR3722077.872509/1‑100 (MQ=60)
                                TTAAATGACAGCGTTGCCAGCGCATCGAGGATGCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTCCAACGCCGATAATCCCGACGATAATTTCCGGCG                                                        >  SRR3722077.150639/1‑100 (MQ=60)
                                TTAAATGACAGCGTTGCCAGCGCATCGAGGATGCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTCCAACGCCGATAATCCCGACGATAATTTCCGGCG                                                        >  SRR3722077.881841/1‑100 (MQ=60)
                                      GACAGCGTTGCCAGCGCATCGAGGATGCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTTCAACGCCGATAATCCCGACGATAATTTCCGGCGGTACTC                                                  >  SRR3722077.859141/1‑100 (MQ=60)
                                      GACAGCGTTGCCAGCGCATCGAGGATGCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTTCAACGCCGATAATCCCGACGATAATTTCCGGCGGTACTC                                                  <  SRR3722077.74978/100‑1 (MQ=60)
                                          GCGTTGCCAGCGCATCGAGGATGCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTCCAACGCCGATAATCCCGACGATAATTTCCGGCGGTACTCCATA                                              >  SRR3722077.1058538/1‑100 (MQ=60)
                                             TTGCCAGCGCATCGAGGATGCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTTCAACGCCGATAATCCCGACGATAATTTCCGGCGGTACTCCATACAC                                           <  SRR3722077.69168/100‑1 (MQ=60)
                                              TGCCAGCGCATCGAGGATGCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTTCAACGCCGATAATCCCGACGATAATTTCCGGCGGTACTCCATACACC                                          <  SRR3722077.21125/100‑1 (MQ=60)
                                                   GCGCATCGAGGATGCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTCCAACGCCGATAATCCCGACGATAATTTCCGGCGGTACTCCATACACCTGCCA                                     <  SRR3722077.455152/100‑1 (MQ=60)
                                                      CATCGAGGATGCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTCCAACGCCGATAATCCCGACGATAATTTCCGGCGGTACTCCATACACCTGCCACGC                                  >  SRR3722077.598639/1‑100 (MQ=60)
                                                             GATGCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTCCAACGCCGATAATCCCGACGATAATTTCCGGCGGTACTCCATACACCTGCCACGCGCGATTC                           >  SRR3722077.259487/1‑100 (MQ=60)
                                                                            CATCACGCGCCCCCAGCGGGTTTCAACGCCGATAATCCCGACGATAATTTCCGGCGGTACTCCATACACCTGCCACGCGCGATTCAACGCATCTTCATAC            <  SRR3722077.464057/100‑1 (MQ=60)
                                                                            CATCACGCGCCCCCAGCGGGTTTCAACGCCGATAATCCCGACGATAATTTCCGGCGGTACTCCATACACCTGCCACGCGCGATTCAACGCATCTTCATAC            <  SRR3722077.440917/100‑1 (MQ=60)
                                                                            CATCACGCGCCCCCAGCGGGTTCCAACGCCGATAATCCCGACGATAATTTCCGGCGGTACTCCGTACACCTGCCACGCGCGATTCAACGCATCTTCATAC            <  SRR3722077.764821/100‑1 (MQ=60)
                                                                               CACGCGCCCCCAGCGGGTTTCAACGCCGATAATCCCGACGATAATTTCCGGCGGTACTCCATACACCTGCCACGCGCGATTCAACGCATCTTCATACTGA         >  SRR3722077.282236/1‑100 (MQ=60)
                                                                                      CCCCAGCGGGTTTCAACGCCGATAATCCCGACGATAATTTCCGGCGGTACTCCATACACCTGCCACGCGCGATTCAACGCATCTTCATACTGATTCCAGA  <  SRR3722077.648552/100‑1 (MQ=60)
                                                                                                  |                                                                                       
CGCCAGAGAAATACTCCGCGCGGCGTGGGTAGTTAAATGACAGCGTTGCCAGCGCATCGAGGATGCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTTCAACGCCGATAATCCCGACGATAATTTCCGGCGGTACTCCATACACCTGCCACGCGCGATTCAACGCATCTTCATACTGATTCCAGA  >  NZ_CP009273/2818353‑2818538

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑